Add I_n (informativeness for assignment) to marker table #56
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Sep 11, 2024
Previously the `usa` panel included 100 loci for which there was *supposed* to be allele frequency data for all 19 sub-populations in a mock population roughly matching demographics in the United States. Due to a bug in that code, some loci in the panel do not have allele frequency data available for all populations. Also, since the initial panel slated for evaluation on real data (`beta`) contains 50 loci, it makes sense to restrict the `usa` panel to 50 loci as well. This update fixes the bug and limits the panel to the top 50 loci ranked by A<sub>e</sub>. Related to #55.
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This update includes the results from a recent re-run of the USA8k Snakemake workflow, with the following changes. - 150k reads simulated per sample rather than 250k reads - new 50-microhap USA panel (see #56)
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This update uses Noah Rosenberg's infocalc script for calculating In for each marker from 1000 Genomes Project Phase 3 genotypes. This provides another criterion (in addition to AvgAe) for ranking markers for different forensic purposes.